Starting phenix.real_space_refine on Sun Dec 29 04:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv2_27006/12_2024/8cv2_27006.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 Na 6 4.78 5 C 6459 2.51 5 N 1578 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Time building chain proxies: 6.52, per 1000 atoms: 0.66 Number of scatterers: 9882 At special positions: 0 Unit cell: (109.056, 105.648, 80.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 Na 6 11.00 O 1776 8.00 N 1578 7.00 C 6459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 84.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.542A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 4.029A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.547A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.898A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.053A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.803A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.838A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 117 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.546A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 117 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.596A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.546A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.541A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 783 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3092 1.34 - 1.46: 1443 1.46 - 1.58: 5371 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 10023 Sorted by residual: bond pdb=" N GLU C 274 " pdb=" CA GLU C 274 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.20e+00 bond pdb=" N GLU B 274 " pdb=" CA GLU B 274 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.26e-02 6.30e+03 5.97e+00 bond pdb=" N GLU A 274 " pdb=" CA GLU A 274 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.26e-02 6.30e+03 5.79e+00 bond pdb=" N SER C 331 " pdb=" CA SER C 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.10e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.09e+00 ... (remaining 10018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 13080 1.15 - 2.30: 413 2.30 - 3.45: 73 3.45 - 4.60: 27 4.60 - 5.74: 15 Bond angle restraints: 13608 Sorted by residual: angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU A 471 " pdb=" CG GLU A 471 " pdb=" CD GLU A 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" O GLU C 274 " ideal model delta sigma weight residual 120.24 117.74 2.50 1.11e+00 8.12e-01 5.06e+00 angle pdb=" CA SER A 331 " pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 120.57 117.90 2.67 1.20e+00 6.94e-01 4.96e+00 ... (remaining 13603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5287 15.74 - 31.48: 512 31.48 - 47.22: 177 47.22 - 62.96: 21 62.96 - 78.70: 6 Dihedral angle restraints: 6003 sinusoidal: 2280 harmonic: 3723 Sorted by residual: dihedral pdb=" CA VAL C 299 " pdb=" C VAL C 299 " pdb=" N ILE C 300 " pdb=" CA ILE C 300 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 299 " pdb=" C VAL B 299 " pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1130 0.029 - 0.058: 378 0.058 - 0.087: 156 0.087 - 0.116: 46 0.116 - 0.145: 15 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CA VAL B 411 " pdb=" N VAL B 411 " pdb=" C VAL B 411 " pdb=" CB VAL B 411 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL C 411 " pdb=" N VAL C 411 " pdb=" C VAL C 411 " pdb=" CB VAL C 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1722 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 401 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA C 401 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA C 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR C 402 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 296 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C HIS C 296 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS C 296 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 297 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 401 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ALA A 401 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.011 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2453 2.80 - 3.33: 9997 3.33 - 3.85: 16120 3.85 - 4.38: 18160 4.38 - 4.90: 32528 Nonbonded interactions: 79258 Sorted by model distance: nonbonded pdb=" NH2 ARG C 39 " pdb=" O VAL C 273 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG A 39 " pdb=" O VAL A 273 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG B 39 " pdb=" O VAL B 273 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP C 368 " pdb="NA NA C 602 " model vdw 2.321 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.322 2.470 ... (remaining 79253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10023 Z= 0.196 Angle : 0.533 5.744 13608 Z= 0.297 Chirality : 0.037 0.145 1725 Planarity : 0.004 0.033 1665 Dihedral : 14.128 78.698 3603 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1287 helix: 1.83 (0.16), residues: 1029 sheet: 1.73 (0.53), residues: 48 loop : -1.87 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS C 41 PHE 0.011 0.001 PHE C 341 TYR 0.009 0.001 TYR B 373 ARG 0.005 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.205 Fit side-chains REVERT: A 274 GLU cc_start: 0.7289 (pm20) cc_final: 0.6901 (pm20) REVERT: B 205 MET cc_start: 0.8442 (ptm) cc_final: 0.8216 (ptm) REVERT: B 258 MET cc_start: 0.8659 (ttm) cc_final: 0.8437 (ttp) REVERT: B 274 GLU cc_start: 0.7284 (pm20) cc_final: 0.6752 (pm20) REVERT: B 473 MET cc_start: 0.7174 (ttp) cc_final: 0.6904 (ttm) REVERT: C 274 GLU cc_start: 0.7233 (pm20) cc_final: 0.6833 (pm20) REVERT: C 449 MET cc_start: 0.8214 (ttp) cc_final: 0.7898 (tmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.3523 time to fit residues: 192.2012 Evaluate side-chains 125 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10023 Z= 0.222 Angle : 0.525 5.635 13608 Z= 0.284 Chirality : 0.038 0.130 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.792 18.012 1365 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.14 % Allowed : 15.60 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.23), residues: 1287 helix: 2.28 (0.16), residues: 1011 sheet: 1.62 (0.53), residues: 48 loop : -0.88 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.002 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.004 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.248 Fit side-chains REVERT: A 274 GLU cc_start: 0.7124 (pm20) cc_final: 0.6833 (pm20) REVERT: A 330 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7735 (mt) REVERT: B 274 GLU cc_start: 0.7186 (pm20) cc_final: 0.6858 (pm20) REVERT: B 330 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7701 (mt) REVERT: B 442 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7679 (tp) REVERT: C 274 GLU cc_start: 0.7191 (pm20) cc_final: 0.6898 (pm20) REVERT: C 449 MET cc_start: 0.8164 (ttp) cc_final: 0.7815 (tmt) outliers start: 34 outliers final: 12 residues processed: 153 average time/residue: 1.3731 time to fit residues: 224.7001 Evaluate side-chains 138 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10023 Z= 0.248 Angle : 0.544 6.183 13608 Z= 0.294 Chirality : 0.039 0.154 1725 Planarity : 0.004 0.034 1665 Dihedral : 3.915 18.442 1365 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.86 % Allowed : 16.99 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.23), residues: 1287 helix: 2.22 (0.16), residues: 1011 sheet: 1.38 (0.53), residues: 48 loop : -0.80 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.002 PHE B 314 TYR 0.008 0.001 TYR A 373 ARG 0.004 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.167 Fit side-chains REVERT: A 274 GLU cc_start: 0.7048 (pm20) cc_final: 0.6793 (pm20) REVERT: A 330 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 274 GLU cc_start: 0.7045 (pm20) cc_final: 0.6699 (pm20) REVERT: B 442 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (tp) REVERT: C 39 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7368 (ttt90) REVERT: C 274 GLU cc_start: 0.7065 (pm20) cc_final: 0.6689 (pm20) outliers start: 31 outliers final: 15 residues processed: 159 average time/residue: 1.2944 time to fit residues: 220.4348 Evaluate side-chains 151 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN B 322 GLN C 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10023 Z= 0.197 Angle : 0.501 5.672 13608 Z= 0.272 Chirality : 0.038 0.144 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.823 18.234 1365 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.05 % Allowed : 17.27 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.23), residues: 1287 helix: 2.35 (0.16), residues: 1011 sheet: 1.37 (0.55), residues: 48 loop : -1.03 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.008 0.001 TYR A 373 ARG 0.005 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7073 (pm20) cc_final: 0.6863 (pm20) REVERT: A 330 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 274 GLU cc_start: 0.7027 (pm20) cc_final: 0.6744 (pm20) REVERT: B 330 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 442 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7754 (tp) REVERT: C 39 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7192 (ttt90) REVERT: C 274 GLU cc_start: 0.7042 (pm20) cc_final: 0.6659 (pm20) outliers start: 33 outliers final: 18 residues processed: 147 average time/residue: 1.4231 time to fit residues: 224.7406 Evaluate side-chains 151 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN B 322 GLN C 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10023 Z= 0.206 Angle : 0.509 6.105 13608 Z= 0.276 Chirality : 0.038 0.139 1725 Planarity : 0.004 0.030 1665 Dihedral : 3.815 17.715 1365 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.05 % Allowed : 18.10 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.23), residues: 1287 helix: 2.34 (0.16), residues: 1011 sheet: 1.31 (0.54), residues: 48 loop : -1.22 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.162 Fit side-chains REVERT: A 274 GLU cc_start: 0.7212 (pm20) cc_final: 0.6976 (pm20) REVERT: A 330 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7697 (mt) REVERT: B 39 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7442 (ttm-80) REVERT: B 258 MET cc_start: 0.8619 (ttm) cc_final: 0.8176 (ttm) REVERT: B 274 GLU cc_start: 0.6937 (pm20) cc_final: 0.6592 (pm20) REVERT: B 330 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7679 (mt) REVERT: B 442 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7746 (tp) REVERT: C 39 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6873 (ttm-80) REVERT: C 229 MET cc_start: 0.8867 (mtp) cc_final: 0.8645 (mtp) REVERT: C 274 GLU cc_start: 0.7039 (pm20) cc_final: 0.6683 (pm20) outliers start: 33 outliers final: 21 residues processed: 148 average time/residue: 1.3153 time to fit residues: 208.9057 Evaluate side-chains 156 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10023 Z= 0.163 Angle : 0.473 4.958 13608 Z= 0.256 Chirality : 0.037 0.165 1725 Planarity : 0.003 0.032 1665 Dihedral : 3.711 17.326 1365 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.68 % Allowed : 18.47 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.23), residues: 1287 helix: 2.50 (0.16), residues: 1011 sheet: 1.35 (0.55), residues: 48 loop : -1.30 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE A 240 TYR 0.009 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.246 Fit side-chains REVERT: A 274 GLU cc_start: 0.7141 (pm20) cc_final: 0.6877 (pm20) REVERT: A 330 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 274 GLU cc_start: 0.6921 (pm20) cc_final: 0.6662 (pm20) REVERT: B 330 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7627 (mt) REVERT: B 442 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7609 (tp) REVERT: C 39 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6833 (ttm-80) REVERT: C 274 GLU cc_start: 0.7049 (pm20) cc_final: 0.6724 (pm20) outliers start: 29 outliers final: 16 residues processed: 150 average time/residue: 1.3892 time to fit residues: 222.2395 Evaluate side-chains 152 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10023 Z= 0.219 Angle : 0.524 5.973 13608 Z= 0.283 Chirality : 0.038 0.166 1725 Planarity : 0.004 0.031 1665 Dihedral : 3.816 17.557 1365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.68 % Allowed : 18.74 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.23), residues: 1287 helix: 2.38 (0.16), residues: 1011 sheet: 1.29 (0.55), residues: 48 loop : -1.38 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.002 PHE A 240 TYR 0.012 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.153 Fit side-chains REVERT: A 274 GLU cc_start: 0.7190 (pm20) cc_final: 0.6908 (pm20) REVERT: A 330 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7683 (mt) REVERT: B 274 GLU cc_start: 0.6994 (pm20) cc_final: 0.6658 (pm20) REVERT: B 330 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7676 (mt) REVERT: B 442 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7748 (tp) REVERT: C 39 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6892 (ttm-80) REVERT: C 274 GLU cc_start: 0.7011 (pm20) cc_final: 0.6644 (pm20) outliers start: 29 outliers final: 20 residues processed: 146 average time/residue: 1.3250 time to fit residues: 206.8975 Evaluate side-chains 153 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10023 Z= 0.170 Angle : 0.486 5.606 13608 Z= 0.261 Chirality : 0.037 0.165 1725 Planarity : 0.004 0.034 1665 Dihedral : 3.725 17.097 1365 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.31 % Allowed : 19.21 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.23), residues: 1287 helix: 2.52 (0.16), residues: 1011 sheet: 1.33 (0.55), residues: 48 loop : -1.40 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.200 Fit side-chains REVERT: A 274 GLU cc_start: 0.7167 (pm20) cc_final: 0.6949 (pm20) REVERT: A 330 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7608 (mt) REVERT: B 274 GLU cc_start: 0.7069 (pm20) cc_final: 0.6736 (pm20) REVERT: B 330 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 442 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7629 (tp) REVERT: C 39 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6799 (ttm-80) REVERT: C 274 GLU cc_start: 0.7060 (pm20) cc_final: 0.6686 (pm20) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 1.3342 time to fit residues: 208.2537 Evaluate side-chains 153 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10023 Z= 0.171 Angle : 0.495 6.889 13608 Z= 0.264 Chirality : 0.037 0.162 1725 Planarity : 0.004 0.034 1665 Dihedral : 3.688 16.965 1365 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.40 % Allowed : 19.58 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.23), residues: 1287 helix: 2.55 (0.16), residues: 1011 sheet: 1.32 (0.55), residues: 48 loop : -1.40 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.978 Fit side-chains REVERT: A 274 GLU cc_start: 0.7172 (pm20) cc_final: 0.6942 (pm20) REVERT: A 330 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7565 (mt) REVERT: B 274 GLU cc_start: 0.7032 (pm20) cc_final: 0.6728 (pm20) REVERT: B 330 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7625 (mt) REVERT: B 431 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6898 (mp0) REVERT: B 442 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7588 (tp) REVERT: C 39 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6848 (ttm-80) REVERT: C 274 GLU cc_start: 0.7070 (pm20) cc_final: 0.6681 (pm20) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 1.3467 time to fit residues: 207.3968 Evaluate side-chains 152 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 449 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 109 optimal weight: 8.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10023 Z= 0.139 Angle : 0.467 7.344 13608 Z= 0.246 Chirality : 0.036 0.154 1725 Planarity : 0.003 0.037 1665 Dihedral : 3.539 16.303 1365 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.03 % Allowed : 20.04 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.23), residues: 1287 helix: 2.73 (0.16), residues: 1011 sheet: 1.26 (0.55), residues: 48 loop : -1.41 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 256 HIS 0.000 0.000 HIS B 296 PHE 0.008 0.001 PHE C 218 TYR 0.007 0.001 TYR A 373 ARG 0.007 0.000 ARG B 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.172 Fit side-chains REVERT: A 274 GLU cc_start: 0.7166 (pm20) cc_final: 0.6897 (pm20) REVERT: A 330 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7510 (mt) REVERT: B 205 MET cc_start: 0.8390 (ptm) cc_final: 0.8154 (ptm) REVERT: B 274 GLU cc_start: 0.7000 (pm20) cc_final: 0.6709 (pm20) REVERT: B 330 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7540 (mt) REVERT: B 431 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6886 (mp0) REVERT: B 442 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7458 (tp) REVERT: C 39 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7266 (ttt90) REVERT: C 274 GLU cc_start: 0.7040 (pm20) cc_final: 0.6751 (pm20) outliers start: 22 outliers final: 12 residues processed: 145 average time/residue: 1.2513 time to fit residues: 195.0599 Evaluate side-chains 145 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 449 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112444 restraints weight = 10153.085| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.06 r_work: 0.3167 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10023 Z= 0.177 Angle : 0.500 8.971 13608 Z= 0.265 Chirality : 0.037 0.157 1725 Planarity : 0.004 0.038 1665 Dihedral : 3.620 17.086 1365 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.75 % Allowed : 20.96 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.23), residues: 1287 helix: 2.64 (0.16), residues: 1011 sheet: 1.67 (0.56), residues: 51 loop : -1.53 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.007 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.04 seconds wall clock time: 69 minutes 21.13 seconds (4161.13 seconds total)